ChIP for sensitive & fast genomic mapping
Chromatin profiling assays enable the mapping of protein-DNA interactions that influence chromatin modeling and gene expression.
Over the years, Chromatin ImmunoPrecipitation (ChIP) assays became the gold-standard for studying transcription factor–DNA binding interactions, nucleosome dynamics, and epigenetics (ex. histone post-translational modifications (PTMs)). This post aims at introducing the latest evolution of ChIP assays: CUTANA™ CUT&RUN and ChIC assays.
Over the last years, ChIP experts express the need for more sensitivity, faster protocols, and more reproducible results (and ideally starting from less starting cellular material). These expectations led to the emergence of new experimental antibody-based experimental approaches like Chromatin ImmunoCleavage (ChIC) assays, and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) methods.
CUTANA™ New ChIP assays
Based on ChIC / CUT&RUN technologies, CUTANA™ product line (developed by Epicypher and distributed by tebu-bio) is a novel ultra-sensitive genomic mapping assay that uses a proprietary immunotethering approach.
Similar to ChIC and CUT&RUN methods, it allows the fast mapping histone PTMs and chromatin interactors with high resolution.
CUTANA™ ChIP principle and advantages
This new approach leverages a factor specific antibody to tether a fusion of protein A, protein G and micrococcal nuclease (pAG-MNase) to genomic binding sites in intact cells, which is then activated by the addition of calcium to cleave DNA. The assay is performed in less than 4 days.
Compared to ChIP-seq assay, CUTANA™ assays have:
- lower sequencing requirements (Sequencing reads required: 3 million),
- improved signal-to-noise, reduced assay time (from cells to data in less than 4 days with < 1day of protocol time)
- less starting cellular material (100 cells required only as described by Dirks et al. in 2016 (Clin Epigenetics; 2016 (Nov 21); 8 :122).
Additionally, CUTANA™ assays save 5-10x in sequencing requirements
and generate superior quality data compared to ChIP-seq using as little as 3 million sequencing reads.
Cells (or nuclei) are immobilized on lectin-coated magnetic beads, permeabilized, and incubated with an antibody to a chromatin target (e.g. histone PTM or chromatin / DNA binding protein). Next, pAG-MNase is added and activated via Ca2+. The clipped chromatin fragments diffuse out, followed by DNA purification and next-generation sequencing.
ChIP assays: pAG-MNase now available!
The pAG-MNase enzyme is the first reagent in the CUTANA™ product line and is available now from tebu-bio CUT&RUN & ChIC assays.
Recombinantly produced in E. coli, CUTANA™ pAG-MNase is a fusion of Proteins A and G to Micrococcal Nuclease and contains a C-terminal 6xHis epitope tag. 2 sizes are available:
Coming soon! CUTANA™ pAG-MNase assay kit for ChIC / CUT&RUN, as well as CUTANA ™ pAG-Tn5 enzyme and assay kit for ChIC / CUT&TAG will be released. So stay tuned!
ChIP related products
- ChIP validated antibodies
- Recombinant human mononucleosomes
- Chromatin remodeling enzymes and substrates
- Histone octamers and recombinant histones
CUTANA™ is a proprietary technology based on chromatin immunocleavage (ChIC) (US20070009937A1; Schmid et. al, Mol Cell 2004) and cleavage Under Targets and Release Using Nuclease (CUT&RUN) (patent pending; Skene and Henikoff, eLIFE 2017) methodology.